Job ID = 4289565 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,177,193 reads read : 6,177,193 reads written : 6,177,193 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:40 6177193 reads; of these: 6177193 (100.00%) were unpaired; of these: 4057373 (65.68%) aligned 0 times 1641673 (26.58%) aligned exactly 1 time 478147 (7.74%) aligned >1 times 34.32% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1769740 / 2119820 = 0.8349 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 14:50:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:50:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:51:01: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:51:01: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:51:01: #1 total tags in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:51:01: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:51:01: #1 tags after filtering in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:01: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:01: #2 number of paired peaks: 170 WARNING @ Tue, 10 Dec 2019 14:51:01: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 10 Dec 2019 14:51:01: start model_add_line... INFO @ Tue, 10 Dec 2019 14:51:02: start X-correlation... INFO @ Tue, 10 Dec 2019 14:51:02: end of X-cor INFO @ Tue, 10 Dec 2019 14:51:02: #2 finished! INFO @ Tue, 10 Dec 2019 14:51:02: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 14:51:02: #2 alternative fragment length(s) may be 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 bps INFO @ Tue, 10 Dec 2019 14:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05_model.r WARNING @ Tue, 10 Dec 2019 14:51:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:51:02: #2 You may need to consider one of the other alternative d(s): 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 WARNING @ Tue, 10 Dec 2019 14:51:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 14:51:02: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:51:03: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.05_summits.bed INFO @ Tue, 10 Dec 2019 14:51:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 14:51:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:51:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:51:32: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:51:32: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:51:32: #1 total tags in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:51:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:51:32: #1 tags after filtering in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:32: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:32: #2 number of paired peaks: 170 WARNING @ Tue, 10 Dec 2019 14:51:32: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 10 Dec 2019 14:51:32: start model_add_line... INFO @ Tue, 10 Dec 2019 14:51:32: start X-correlation... INFO @ Tue, 10 Dec 2019 14:51:32: end of X-cor INFO @ Tue, 10 Dec 2019 14:51:32: #2 finished! INFO @ Tue, 10 Dec 2019 14:51:32: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 14:51:32: #2 alternative fragment length(s) may be 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 bps INFO @ Tue, 10 Dec 2019 14:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10_model.r WARNING @ Tue, 10 Dec 2019 14:51:32: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:51:32: #2 You may need to consider one of the other alternative d(s): 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 WARNING @ Tue, 10 Dec 2019 14:51:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 14:51:32: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:51:33: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.10_summits.bed INFO @ Tue, 10 Dec 2019 14:51:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 14:51:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:51:59: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:52:03: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:52:03: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:52:03: #1 total tags in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:52:03: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:52:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:52:03: #1 tags after filtering in treatment: 350080 INFO @ Tue, 10 Dec 2019 14:52:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:52:03: #1 finished! INFO @ Tue, 10 Dec 2019 14:52:03: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:52:03: #2 number of paired peaks: 170 WARNING @ Tue, 10 Dec 2019 14:52:03: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 10 Dec 2019 14:52:03: start model_add_line... INFO @ Tue, 10 Dec 2019 14:52:03: start X-correlation... INFO @ Tue, 10 Dec 2019 14:52:03: end of X-cor INFO @ Tue, 10 Dec 2019 14:52:03: #2 finished! INFO @ Tue, 10 Dec 2019 14:52:03: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 14:52:03: #2 alternative fragment length(s) may be 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 bps INFO @ Tue, 10 Dec 2019 14:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20_model.r WARNING @ Tue, 10 Dec 2019 14:52:03: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:52:03: #2 You may need to consider one of the other alternative d(s): 52,132,154,172,210,240,265,282,288,404,418,501,531,548,591 WARNING @ Tue, 10 Dec 2019 14:52:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 14:52:03: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:52:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:52:04: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932549/SRX6932549.20_summits.bed INFO @ Tue, 10 Dec 2019 14:52:05: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling